[AMBER] diffusion path length

From: newamber list <newamberlist.gmail.com>
Date: Fri, 11 Jul 2014 20:11:03 +0100

Hi All

I have some general query regarding diffusion. cpptraj diffusion command
 'In order to correctly calculate diffusion molecules should take
continuous paths'

Ideally how long this path should be? infinite or some finite (if finite,
then how much?). I am asking because somehow I am interested to know local
diffusion in very small volume and as its a very small volume so one can
not expect the same molecule to stay longer inside that volume and
molecules will be exchanging quickly with molecules outside the considered
box. Thus smaller will be the continuous path it will travel if moves out
volume quickly.

Any suggestions will be really helpful

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Received on Fri Jul 11 2014 - 12:30:03 PDT
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